Release 2025

.github/workflows/conda-package-build.yml

@@ -1,21 +1,25 @@
-name: Building Package
+name: OpenAlea CI
 
 on:
   push:
     branches:
-      - '**'
+      - main
+      - master
     tags:
       - 'v*'
   pull_request:
-    branches:
-      - '**'
-
+    types:
+      - opened
+      - synchronize
+      - reopened
+  release:
+    types:
+      - published
 
 jobs:
   build:
-    uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
+    uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
     with:
-      python-minor-version: '[8,9,10,11]'
-      build-options: ''
+      conda-directory: "./stat_tool/conda"
     secrets:
       anaconda_token: ${{ secrets.ANACONDA_TOKEN }}

sequence_analysis/test/functional1.py

@@ -8,25 +8,25 @@
 import os
 from openalea.stat_tool import *
 from openalea.sequence_analysis import *
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
-seq1 = Sequences(get_shared_data( 'dupreziana_20a2.seq'))   # correct
+seq1 = Sequences(str(get_shared_data( 'dupreziana_20a2.seq')))   # correct
 seq2 = RemoveRun(seq1, 1, 0, "End")              # correct
 
 histo21 = ExtractHistogram(seq2, "Recurrence", 1)  # correct
 histo22 = ExtractHistogram(seq2, "Recurrence", 2)  # correct
 
-seq3 = Sequences(get_shared_data( 'dupreziana_40a2.seq'))   #correct
+seq3 = Sequences(str(get_shared_data( 'dupreziana_40a2.seq')))   #correct
 seq4_0 = RemoveRun(seq3, 2, 0, "End")            #correct
 seq4 = SegmentationExtract(seq4_0, 1, 2)         #correct
 
 
-seq5 = Sequences(get_shared_data( 'dupreziana_60a2.seq'))   #correct
+seq5 = Sequences(str(get_shared_data( 'dupreziana_60a2.seq')))   #correct
 seq6_0 = RemoveRun(seq5, 2, 0, "End")            #correct
 seq6 = LengthSelect(SegmentationExtract(seq6_0, 1, 2), 1, Mode="Reject") #correct
 
 
-seq7 = Sequences(get_shared_data( 'dupreziana_80a2.seq'))   #correct
+seq7 = Sequences(str(get_shared_data( 'dupreziana_80a2.seq')))   #correct
 seq8_0 = RemoveRun(seq7, 2, 0, "End")            #correct
 seq8 = SegmentationExtract(seq8_0, 1, 2)         #correct
 
@@ -85,7 +85,7 @@
 
 
 # test #
-hmc9 = HiddenVariableOrderMarkov(get_shared_data( "dupreziana21.hc"))
+hmc9 = HiddenVariableOrderMarkov(str(get_shared_data( "dupreziana21.hc")))
 hmc10 = Estimate(seq10, "HIDDEN_VARIABLE_ORDER_MARKOV", hmc9, GlobalInitialTransition=True, NbIteration=80)
 hmc11 = Estimate(seq10, "HIDDEN_VARIABLE_ORDER_MARKOV", hmc9, GlobalInitialTransition=False, NbIteration=80)
 

sequence_analysis/test/functional2.py

@@ -8,16 +8,16 @@
 from openalea.sequence_analysis import *
 from openalea.sequence_analysis.estimate import  Estimate
 from openalea.sequence_analysis.compare import  Compare
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 
-seq20 = Sequences(get_shared_data("belren1.seq"))
-seq21 = Sequences(get_shared_data("elstar1.seq"))
-seq22 = Sequences(get_shared_data("fuji1.seq"))
-seq23 = Sequences(get_shared_data("gala1.seq"))
-seq24 = Sequences(get_shared_data("granny1.seq"))
-seq25 = Sequences(get_shared_data("reinet1.seq"))
-seq26 = Sequences(get_shared_data("wij1.seq"))
+seq20 = Sequences(str(get_shared_data("belren1.seq")))
+seq21 = Sequences(str(get_shared_data("elstar1.seq")))
+seq22 = Sequences(str(get_shared_data("fuji1.seq")))
+seq23 = Sequences(str(get_shared_data("gala1.seq")))
+seq24 = Sequences(str(get_shared_data("granny1.seq")))
+seq25 = Sequences(str(get_shared_data("reinet1.seq")))
+seq26 = Sequences(str(get_shared_data("wij1.seq")))
 
 Display(seq25, ViewPoint="Data")
 Plot(seq25, "Intensity")
@@ -52,7 +52,7 @@
 matrix30 = Compare(seq32)
 matrix31 = Compare(seq32, VectorDistance("S"))
 matrix32 = Compare(seq32, VectorDistance("S"), Transposition=True)
-matrix33 = Compare(seq32, VectorDistance(get_shared_data("test_align1.a")), Transposition=True)
+matrix33 = Compare(seq32, VectorDistance(str(get_shared_data("test_align1.a"))), Transposition=True)
 
 Display(Clustering(matrix33, "Partition", 2))
 Clustering(matrix33, "Hierarchy", Algorithm="Agglomerative")
@@ -76,22 +76,22 @@
 Plot(seq25, 14, 6, "Multinomial", ViewPoint="SegmentProfile", Output="ChangePoint")
 # hidden semi-Markov chains
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("belren1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("belren1.hsc")))
 hsmc20 = Estimate(seq20, "HIDDEN_SEMI-MARKOV", hsmc0)
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("elstar1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("elstar1.hsc")))
 hsmc21 = Estimate(seq21, "HIDDEN_SEMI-MARKOV", hsmc0)
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("fuji1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("fuji1.hsc")))
 hsmc22 = Estimate(seq22, "HIDDEN_SEMI-MARKOV", hsmc0)
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("gala1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("gala1.hsc")))
 hsmc23 = Estimate(seq23, "HIDDEN_SEMI-MARKOV", hsmc0)
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("granny1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("granny1.hsc")))
 hsmc24 = Estimate(seq24, "HIDDEN_SEMI-MARKOV", hsmc0)
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("reinet1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("reinet1.hsc")))
 hsmc25 = Estimate(seq25, "HIDDEN_SEMI-MARKOV", hsmc0)
 
 Display(hsmc25)
@@ -112,7 +112,7 @@
 seq25_1 = ExtractData(hsmc25)
 Display(seq25_1, ViewPoint="Data", Format="Line")
 
-hsmc0 = HiddenSemiMarkov(get_shared_data("wij1.hsc"))
+hsmc0 = HiddenSemiMarkov(str(get_shared_data("wij1.hsc")))
 hsmc26 = Estimate(seq26, "HIDDEN_SEMI-MARKOV", hsmc0)
 
 # model comparison

sequence_analysis/test/functional3.py

@@ -26,8 +26,9 @@
 from openalea.sequence_analysis import *
 from openalea.sequence_analysis.estimate import  Estimate
 from openalea.sequence_analysis.compare import  Compare
+from tools import runTestClass, robust_path as get_shared_data
 
-seq69 = Sequences(get_shared_data( "pin_laricio_7x.seq"))
+seq69 = Sequences(str(get_shared_data( "pin_laricio_7x.seq")))
 seq70 = Cluster(seq69, "Step", 1, 10)
 #seq70 = IndexParameterExtract(Cluster(seq69, "Step", 2, 10), 1927, MaxIndex=1992)
 
@@ -130,10 +131,10 @@
 
 # estimation of a hidden semi-Markov chain
 
-hmc60 = HiddenSemiMarkov(get_shared_data( "pin_laricio_6.hsc"))
+hmc60 = HiddenSemiMarkov(str(get_shared_data( "pin_laricio_6.hsc")))
 hmc6 = Estimate(seq70, "HIDDEN_SEMI-MARKOV", hmc60)
 
-hsmc60 = HiddenSemiMarkov(get_shared_data( "pin_laricio_6.hsc"))
+hsmc60 = HiddenSemiMarkov(str(get_shared_data( "pin_laricio_6.hsc")))
 hsmc6 = Estimate(seq70, "HIDDEN_SEMI-MARKOV", hsmc60)
 hsmc61 = Estimate(seq70, "HIDDEN_SEMI-MARKOV", "Ordinary", 6, "LeftRight")
 

sequence_analysis/test/test_add_absorbing_run.py

@@ -9,7 +9,7 @@
 from openalea.sequence_analysis.sequences import Sequences
 from openalea.sequence_analysis.semi_markov import SemiMarkov
 from openalea.sequence_analysis.data_transform import AddAbsorbingRun
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class _AddAbsorbingRun():
     """
@@ -72,7 +72,7 @@ def __init__(self):
         self.max_length = 30
 
     def create_data(self):
-        seq = Sequences(get_shared_data('sequences1.seq'))
+        seq = Sequences(str(get_shared_data('sequences1.seq')))
         return seq
 
 class Test_AddAbsorbingRun_SemiMarkov(_AddAbsorbingRun):
@@ -83,7 +83,11 @@ def __init__(self):
         self.max_length = 1000
 
     def create_data(self):
-        markov = SemiMarkov(get_shared_data('test_semi_markov.dat') )
+        markov = SemiMarkov(str(get_shared_data('test_semi_markov.dat')))
         semi_markov_data = markov.simulation_nb_elements(1, 1000, True)
         return semi_markov_data
 
+if __name__ == "__main__":
+    runTestClass(Test_AddAbsorbingRun_Sequences())
+    runTestClass(Test_AddAbsorbingRun_SemiMarkov())
+

sequence_analysis/test/test_build_auxialiary_variable.py

@@ -1,5 +1,5 @@
 from openalea.sequence_analysis import *
-
+from tools import runTestClass, robust_path as get_shared_data
 
 def test1():
     seq6 = Sequences(str(get_shared_data("pin_laricio_6.seq")))
@@ -16,3 +16,6 @@ def test1():
     # Plot(hsmc30, 1)
     seq31 = BuildAuxiliaryVariable(ExtractData(hsmc30))
     Plot(SelectIndividual(seq31, [95]), ViewPoint="Data")
+
+if __name__ == "__main__":
+    test1()

sequence_analysis/test/test_cluster.py

@@ -15,8 +15,7 @@
 from openalea.stat_tool.compound import Compound
 from openalea.stat_tool.vectors import Vectors
 
-from tools import runTestClass
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class _Cluster():
     """Test class to test cluster function and classes

sequence_analysis/test/test_compare.py

@@ -15,9 +15,7 @@
 from openalea.sequence_analysis.estimate import Estimate
 from openalea.sequence_analysis.data_transform import Thresholding
 
-from openalea.sequence_analysis import get_shared_data
-from tools import runTestClass
-
+from tools import runTestClass, robust_path as get_shared_data
 
 class _Compare():
     """
@@ -41,12 +39,12 @@ def __init__(self):
         self.data = self.create_data()
 
     def create_data(self):
-        seq0 = Sequences(get_shared_data( "chene_sessile_15pa.seq"))
+        seq0 = Sequences(str(get_shared_data( "chene_sessile_15pa.seq")))
         vec10 = Vectors(seq0)
         vec95 = ValueSelect(vec10, 1, 95)
         vec96 = ValueSelect(vec10, 1, 96)
         vec97 = ValueSelect(vec10, 1, 97)
-        return [vec95, vec96, vec97]
+        return([vec95, vec96, vec97])
 
     def test_compare(self):
         seq = self.data
@@ -63,8 +61,8 @@ def __init__(self):
         self.data = self.create_data()
 
     def create_data(self):
-        seq = Sequences(get_shared_data( 'dupreziana_a1.seq'))
-        return seq
+        seq = Sequences(str(get_shared_data( 'dupreziana_a1.seq')))
+        return(seq)
 
     def test_compare(self):
         seq = self.data
@@ -79,8 +77,8 @@ def __init__(self):
         self.data = self.create_data()
 
     def create_data(self):
-        seq = Sequences(get_shared_data( 'dupreziana_a1.seq'))
-        return seq
+        seq = Sequences(str(get_shared_data( 'dupreziana_a1.seq')))
+        return(seq)
 
     def test_compare(self):
         seq = self.data
@@ -96,7 +94,7 @@ def __init__(self):
 
     def create_data(self):
         data = Vectors([[1, 2, 3], [1, 3, 1], [4, 5, 6]])
-        return data
+        return(data)
 
     def test_compare(self):
         data = self.data
@@ -114,13 +112,13 @@ def __init__(self):
         self.data = self.create_data()
 
     def create_data(self):
-        hsmc0 = HiddenSemiMarkov(get_shared_data( "belren1.hsc"))
-        hsmc1 = HiddenSemiMarkov(get_shared_data("elstar1.hsc"))
-        seq0 = Sequences(get_shared_data( "belren1.seq"))
-        seq1 = Sequences(get_shared_data( "elstar1.seq"))
+        hsmc0 = HiddenSemiMarkov(str(get_shared_data( "belren1.hsc")))
+        hsmc1 = HiddenSemiMarkov(str(get_shared_data("elstar1.hsc")))
+        seq0 = Sequences(str(get_shared_data( "belren1.seq")))
+        seq1 = Sequences(str(get_shared_data( "elstar1.seq")))
         data0 = Estimate(seq0, "HIDDEN_SEMI-MARKOV", hsmc0)
         data1 = Estimate(seq1, "HIDDEN_SEMI-MARKOV", hsmc1)
-        return [seq0, seq1, data0, data1]
+        return([seq0, seq1, data0, data1])
 
     def test_compare(self):
         data = self.data

sequence_analysis/test/test_compute_self_transition.py

@@ -6,10 +6,11 @@
 
 
 from openalea.sequence_analysis.data_transform import ComputeSelfTransition
-from openalea.sequence_analysis import Sequences, get_shared_data
+from openalea.sequence_analysis import Sequences
+from tools import runTestClass, robust_path as get_shared_data
 
-seq1 = Sequences(get_shared_data("sequences1.seq"))
-seqn = Sequences(get_shared_data("sequences2.seq"))
+seq1 = Sequences(str(get_shared_data("sequences1.seq")))
+seqn = Sequences(str(get_shared_data("sequences2.seq")))
 
 
 
@@ -24,3 +25,6 @@ def test_ComputeSelfTransition_order():
     the order arguments is protected..."""
     ComputeSelfTransition(seqn, Order=2)
 
+if __name__ == "__main__":
+    test_ComputeSelfTransition()
+    test_ComputeSelfTransition_order()

sequence_analysis/test/test_correlation.py

@@ -16,7 +16,7 @@
 
 from openalea.stat_tool.distribution import Distribution
 from tools import runTestClass
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 class Data():
 
@@ -27,7 +27,7 @@ def __init__(self):
 
     def create_sequence_data(self):
 
-        seq66 = Sequences(get_shared_data( "laricio_date66.seq"))
+        seq66 = Sequences(str(get_shared_data( "laricio_date66.seq")))
         seq69 = MovingAverage(VariableScaling(seq66, 3, 100),
                           Distribution("B", 0, 6, 0.5), BeginEnd=True,
                           Output="Residual")
@@ -37,7 +37,7 @@ def CorrelationData(index=1):
     """Returns a correlation
 
     index from 1 to 3"""
-    seq66 = Sequences(get_shared_data( "laricio_date66.seq"))
+    seq66 = Sequences(str(get_shared_data( "laricio_date66.seq")))
     ret = ComputeCorrelation(seq66, index)
     return ret
 
@@ -62,7 +62,7 @@ def test_correlation_no_optional_arguments(self):
         cf = ComputeCorrelation(seq, self.variable)
 
     def test_spearman(self):
-        seq = Sequences(get_shared_data( "laricio_date66.seq"))
+        seq = Sequences(str(get_shared_data( "laricio_date66.seq")))
         ComputeCorrelation(seq, 1, Type="Spearman")
         ComputeCorrelation(seq, 1, 2,Type="Spearman")
         try:

sequence_analysis/test/test_cumulate.py

@@ -11,11 +11,11 @@
 
 
 from openalea.sequence_analysis.data_transform import Cumulate
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 from openalea.sequence_analysis import Sequences
 
-seqn = Sequences(get_shared_data("sequences2.seq"))
-seq1 = Sequences(get_shared_data("sequences1.seq"))
+seqn = Sequences(str(get_shared_data("sequences2.seq")))
+seq1 = Sequences(str(get_shared_data("sequences1.seq")))
 
 
 

sequence_analysis/test/test_data.py

@@ -1,6 +1,10 @@
-from openalea.sequence_analysis import get_shared_data
+from tools import runTestClass, robust_path as get_shared_data
 
 
 def test_get_shared_data():
     from openalea.sequence_analysis.sequences import Sequences
     seq = Sequences(str(get_shared_data('wij1.seq')))
+    assert(seq)
+
+if __name__ == "__main__":
+    test_get_shared_data()